A link between <scp>KIT</scp> expression, mast cell abundance and activity, and Th2‐high endotype in asthmatic airways
Authors: Nguyen Quoc Vuong Tran, Minh‐Khang Le, Yuki Nakamura, Tetsuo Kondo, Atsuhito Nakao
Journal: Allergy (2023)

The KIT receptor tyrosine kinase is primarily expressed in mature immune cells, predominantly mast cells. Together with its ligand, stem cell factor (SCF), it controls mast cell proliferation and survival.1 In asthma, KIT expression is upregulated in the airways,2 and inhibition of KIT signaling ameliorates both experimental asthma in mice and severe asthma in humans.3, 4 However, a comprehensive analysis of KIT expression in diverse asthma populations remains lacking. This study aims to bridge this gap through an in-depth gene expression analysis of KIT in a public database of patients with asthma. We curated five gene expression data sets from the National Center for Biotechnology Information-Gene Expression Omnibus (NCBI-GEO), namely GSE41861, GSE43696, GSE63142, GSE67472, and GSE89809. All these data sets include bronchial epithelial brushing samples from patients with asthma and healthy subjects (controls). We included two other data sets derived solely from epithelial brushing samples from patients with asthma, GSE76226 and GSE65584, for comparison of KIT-high and KIT-low asthma groups (Table S1). Differential gene expression analysis showed that patients with asthma had higher KIT expression than controls in four out of five data sets (4/5), regardless of asthma severity (Figure 1A). The expressions of KITLG (SCF), IL-25, IL-33, TSLP, IL-4, IL-5, and IL-13, however, were comparable between controls and patients with asthma, except for higher expression of IL-5 and IL-13 in patients with asthma than controls in GSE63142 and GSE41861, respectively (Figure S1). Consistent with KIT expression, two in silico cytometry methods (ssGSEA and CIBERSORTx) showed a higher abundance of mast cells and also Th2 cells in patients with asthma than controls in 5/5 and 4/5 data sets, respectively (Figure 1B; Figure S2A). Interestingly, there were no differences in eosinophils, which could be explained by the heterogeneity of asthma population across data sets, possible low numbers of eosinophils in bronchial epithelial brushing samples, and treatment response. We divided the patients in each data set into two groups based on KIT expression levels: KIT-high (above average) and KIT-low (below average). In the KIT-high group, the two in silico cytometry methods revealed a higher abundance of mast cells and basophils in 6/7 and 4/7 data sets, respectively (Figure 2A; Figure S2B). REACTOME-based pathway analysis showed greater enrichment of the Fc𝜀RI signaling pathway in the KIT-high group across all seven data sets (Figure 2B). Interestingly, high TGF-β signaling activity was observed in the KIT-high group in GSE89809 and GSE76226 compared to the KIT-low group (Figure 2B). There were no differences regarding other signaling pathways (Figure S3). Asthma can be classified as Th2-high or -low. Woodruff et al. reported a useful categorization based on the expression in bronchial epithelial cells of three IL-13-induced genes, CLCA1, POSTN, and SERPINB2.5 Following their findings, we categorized patients in each data set as Th2-high or -low (Figure S4). The Th2-high group had higher expression of IL-13 and KITLG than the Th2-low group in the 4/7 and 5/7 data sets, respectively (Figure S5A). In addition, the Th2-high group had a higher abundance of mast cells (7/7 data sets) and basophils (5/7 data sets), and, to a lesser extent, of Th2 cells (3/7 data sets) and eosinophils (3/7 data sets) than the Th2-low group (Figure S5B). The latter findings might be due to possible low numbers of Th2 cells and eosinophils in bronchial epithelial brushing samples. Of note, across all seven data sets, the KIT-high group, in contrast to the KIT-low group, included predominantly Th2-high individuals (Figure 2C). Collectively, our comprehensive analysis reveals a link between KIT expression, mast cell abundance and activity (FcεRI signaling), and Th2-high endotype in asthmatic airways. Because most patients with asthma in the included data sets, except for GSE67472, were taking asthma drugs (Table S1), the findings indicate that KIT expression and mast cell abundance and activity remain elevated in asthmatic airways regardless of treatment. Thus, the results may reaffirm and reemphasize the importance of KIT or mast cells as therapeutic targets in asthma. There are several limitations to this study. First, we used gene data sets derived from bronchial epithelial brushing samples, making it difficult to evaluate genes or immune cells that are expressed or present in subepithelial microenvironments, respectively (e.g., extracellular matrix components, type 2 cytokines, Th2 cells). Second, asthma treatments may affect immune cell abundance. For instance, eosinophils are sensitive to inhaled cortocosteroids.6 Third, sample collection was probably performed when patients were stable, perhaps complicating the ability to assess the expression of inducible cytokines such as TSLP, IL-25, and IL-33. The study was conceptualized and designed by NQVT and AN. NQVT, KL, and YN screened and selected data sets. The analysis was performed by NQVT under the guidance of AN, while M-KL conducted a double-check with supervision from TK. NQVT and M-KL prepared the figures and tables. NQVT, YN, and AN wrote the manuscript. All authors discussed and interpreted data analysis. AN and TK finalized the manuscript. All authors approved the final version of the manuscript before submission. We thank Ms. Yukino Fukasawa, Ms. Tomoko Tohno, and Ms. Maiko Aihara for their excellent assistance. This research was funded by a grant-in-aid for scientific research to AN from the Ministry of Education, Culture, Sports, Science, and Technology, Japan (grant number 22K19427). The authors declare no conflict of interest in relation to this work. Data sharing is not applicable to this article as no new data were created or analyzed in this study. Data S1. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.